I would think that an inland link would need to have its main trunk connecting from Escondido to Mission Valley, probably mostly following I-15. At the north end, it should tie into the Sprinter, and at the south end into the trolley. It might also extend further south and tie into one or both of the other trolley lines.
Connecting to this, I would -- perhaps somewhat selfishly -- like a connection along Mira Mesa Blvd, connecting to The Coaster at Sorrento Valley. This might extend west, and north, through 4S Ranch and Scripps Ranch into Poway, and East to the UTC transit center. The eastward extension would require a serious hill climb, so it might be easier to put in a new station on the Coaster, or run it well overhead like I-5 and I-805 through Sorrento Valley and put in a long ramp, escalator, or other means of connecting the two lines. If extended to UTC, it could also continue through La Jolla, but there may not be as much demand there.
A second connecting line might be warranted along CA-52, running from the far end of the Trolley to The Coaster or perhaps a loop at the UTC.
As far as what kind of rail technology to use, my first thought was light rail, or semi-light rail. Basically using the same kind of vehicles are used on the Sprinter or possibly on the Trolley. But then I thought about the fact that this line will have to co-exist with roads for most of its run. This would either require an elevated structure or a subway. An elevated structure would be less expensive to build. But California's earthquake problem might eliminate that advantage.
For an elevated, or largely elevated, structure I'm thinking that a monorail might be as good, if not a better, choice than a traditional light rail. If I recall, monorails are less visually intrusive than other light rail structures -- at least the Seattle and Orlando monorails aren't as obvious as the Chicago, New York and Boston elevated trains (I've only seen New York and Boston in pictures, FWIW). And there is at least one, very small, monorail system operating in California so the earthquake issue for them may have been addressed.
So, in my wild dreams, I would like to see a monorail connecting from Escondido to the Trolley Blue Line somewhere in the South Bay, with a cross connection from Poway to the end of the Trolley Orange Line, looping across Mira Mesa to the UTC and then back across Clarmont Mesa. Of course, in the same wild dreams this system would get heavy usage, taking a lot of the cars off of the impacted roads, would have regular scheduling, and would allow for flexible travel throughout metro San Diego.
In my realistic dreams, I suspect that we'll be stuck with the three rail systems we have, plus bus service that will face continual cut backs and doesn't work unless you happen to be going not too far along one of their lines.